{ "cells": [ { "cell_type": "markdown", "id": "9995f4b2-2eb3-4af2-a73e-17e60dd97366", "metadata": {}, "source": [ "# Preliminary analysis of growth data for efflux experiment\n", "\n", "(c) 2024 Justin Bois. This work is licensed under a [Creative Commons Attribution License CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/). All code contained herein is licensed under an [MIT license](https://opensource.org/licenses/MIT).\n", "\n", "This document was prepared at [Caltech](http://www.caltech.edu) with support financial support from the [Donna and Benjamin M. Rosen Bioengineering Center](http://rosen.caltech.edu).\n", "\n", "\n", "\n", "*This tutorial was generated from an Jupyter notebook. You can download the notebook [here](efflux_analysis.ipynb).*\n", "\n", "
" ] }, { "cell_type": "code", "execution_count": 1, "id": "3ed431b3-c1ed-402a-8a69-ba0a3a978403", "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", "
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\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
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\n", "\n", "Here, I begin the analysis the data for the 2024 efflux pump experiment. You need to adjust the code cell below to give the path to your data sets." ] }, { "cell_type": "code", "execution_count": 2, "id": "9447c75b-e4e7-4645-bd56-1b3564a21131", "metadata": {}, "outputs": [], "source": [ "# This is where the data are on my machine. If you are in \n", "# the same directory as the data sets, then you can use\n", "# data_path = './'\n", "data_path = '/Users/bois/Dropbox/bi1x_2024_fall_data/efflux/'" ] }, { "cell_type": "markdown", "id": "974da43e-1c90-4034-b4cc-4a6efd4e4a75", "metadata": {}, "source": [ "## Data wrangling\n", "\n", "We will read in the data. First, the function given in the tutorial." ] }, { "cell_type": "code", "execution_count": 3, "id": "3f04c235-372b-4ef8-bc30-3fc7a9a097e6", "metadata": {}, "outputs": [], "source": [ "def timestamp_to_seconds(t_stamp):\n", " \"\"\"Convert H:M:S string to seconds. This is necessary\n", " to hand-build because the datetime utilities do not handle\n", " times over 24 hours.\"\"\"\n", " h, m, s = t_stamp.split(':')\n", " return 3600 * int(h) + 60 * int(m) + float(s)\n", "\n", "\n", "def read_plate_reader(fname, header_row, last_row):\n", " \"\"\"Read in time series data from Bi 1x plate reader.\n", "\n", " Parameters\n", " ----------\n", " fname : str\n", " Path to file outputted from plate reader.\n", " header_row : int\n", " Number of row containing header column (zero-indexed)\n", " last_row : int\n", " Last row of the file containing the time series data (zero-indexed)\n", "\n", " Returns\n", " -------\n", " output : DataFrame\n", " Polars DataFrame containing time series data.\n", " \"\"\"\n", " # Get relevant contents of file as string\n", " with open(fname, \"r\", encoding=\"ISO-8859-1\") as f:\n", " lines = f.readlines()\n", " file_str = \"\".join(lines[header_row : last_row + 1])\n", "\n", " # How many total lines to read\n", " n_rows = last_row - header_row\n", "\n", " # Read in data frame\n", " df = pl.read_csv(\n", " io.StringIO(file_str),\n", " separator=\"\\t\",\n", " encoding=\"ISO-8859-1\",\n", " )\n", "\n", " # Rename temperature column\n", " T_col = [col for col in df.columns if \"T°\" in col][0]\n", " df = df.rename({T_col: \"temperature (deg C)\"})\n", "\n", " # Parse the time column\n", " df = df.with_columns(\n", " pl.col(\"Time\")\n", " .map_elements(timestamp_to_seconds, return_dtype=float)\n", " .alias(\"time (s)\")\n", " ).with_columns(\n", " pl.col('time (s)') - pl.col('time (s)').min()\n", " )\n", "\n", " # Time in units of hours\n", " df = df.with_columns((pl.col('time (s)') / 3600).alias('time (hr)'))\n", "\n", " return df" ] }, { "cell_type": "markdown", "id": "bbd516a9-e86e-47da-93f6-3ccbe2651cd1", "metadata": {}, "source": [ "Next, we load in the data." ] }, { "cell_type": "code", "execution_count": 4, "id": "8a3abe36-0354-451e-b028-cbaaf7cedf74", "metadata": {}, "outputs": [], "source": [ "fname = os.path.join(data_path, '20241122_efflux.txt')\n", "header_row = 53\n", "last_row = 294\n", "\n", "# Load in data\n", "df = read_plate_reader(fname, header_row, last_row)" ] }, { "cell_type": "markdown", "id": "43fe6b16-af41-45d9-9326-4f8b14616545", "metadata": {}, "source": [ "Now we'll add the metadata, first defining dictionaries." ] }, { "cell_type": "code", "execution_count": 5, "id": "355ffb3b-76ba-4c21-8f72-90f8c209630b", "metadata": {}, "outputs": [], "source": [ "well_metadata = dict(\n", " A1=\"MG-0.0\",\n", " A2=\"WT-0.21\",\n", " A3=\"MG-0.0\",\n", " A4=\"WT-0.90\",\n", " A5=\"MG-0.0\",\n", " A6=\"WT-3.90\",\n", " A7=\"MG-0.0\",\n", " A8=\"WT-16.90\",\n", " A9=\"MG-0.0\",\n", " A10=\"WT-73.15\",\n", " A11=\"MG-0.0\",\n", " A12=\"WT-208.33\",\n", " B1=\"3.19-0.0\",\n", " B2=\"UV5-0.21\",\n", " B3=\"3.19-0.0\",\n", " B4=\"UV5-0.90\",\n", " B5=\"3.19-0.0\",\n", " B6=\"UV5-3.90\",\n", " B7=\"3.19-0.0\",\n", " B8=\"UV5-16.90\",\n", " B9=\"3.19-0.0\",\n", " B10=\"UV5-73.15\",\n", " B11=\"3.19-0.0\",\n", " B12=\"UV5-208.33\",\n", " C1=\"IW-0.0\",\n", " C2=\"MG-0.44\",\n", " C3=\"IW-0.0\",\n", " C4=\"MG-1.88\",\n", " C5=\"IW-0.0\",\n", " C6=\"MG-8.13\",\n", " C7=\"IW-0.0\",\n", " C8=\"MG-35.17\",\n", " C9=\"IW-0.0\",\n", " C10=\"MG-152.19\",\n", " C11=\"IW-0.0\",\n", " C12=\"MG-312.50\",\n", " D1=\"WT-0.0\",\n", " D2=\"3.19-0.44\",\n", " D3=\"WT-0.0\",\n", " D4=\"3.19-1.88\",\n", " D5=\"WT-0.0\",\n", " D6=\"3.19-8.13\",\n", " D7=\"WT-0.0\",\n", " D8=\"3.19-35.17\",\n", " D9=\"WT-0.0\",\n", " D10=\"3.19-152.19\",\n", " D11=\"WT-0.0\",\n", " D12=\"3.19-312.50\",\n", " E1=\"UV5-0.0\",\n", " E2=\"IW-0.44\",\n", " E3=\"UV5-0.0\",\n", " E4=\"IW-1.88\",\n", " E5=\"UV5-0.0\",\n", " E6=\"IW-8.13\",\n", " E7=\"UV5-0.0\",\n", " E8=\"IW-35.17\",\n", " E9=\"UV5-0.0\",\n", " E10=\"IW-152.19\",\n", " E11=\"UV5-0.0\",\n", " E12=\"IW-312.50\",\n", " F1=\"MG-0.21\",\n", " F2=\"WT-0.44\",\n", " F3=\"MG-0.90\",\n", " F4=\"WT-1.88\",\n", " F5=\"MG-3.90\",\n", " F6=\"WT-8.13\",\n", " F7=\"MG-16.90\",\n", " F8=\"WT-35.17\",\n", " F9=\"MG-73.15\",\n", " F10=\"WT-152.19\",\n", " F11=\"MG-208.33\",\n", " F12=\"WT-312.50\",\n", " G1=\"3.19-0.21\",\n", " G2=\"UV5-0.44\",\n", " G3=\"3.19-0.90\",\n", " G4=\"UV5-1.88\",\n", " G5=\"3.19-3.90\",\n", " G6=\"UV5-8.13\",\n", " G7=\"3.19-16.90\",\n", " G8=\"UV5-35.17\",\n", " G9=\"3.19-73.15\",\n", " G10=\"UV5-152.19\",\n", " G11=\"3.19-208.33\",\n", " G12=\"UV5-312.50\",\n", " H1=\"IW-0.21\",\n", " H2=\"blank\",\n", " H3=\"IW-0.90\",\n", " H4=\"blank\",\n", " H5=\"IW-3.90\",\n", " H6=\"blank\",\n", " H7=\"IW-16.90\",\n", " H8=\"blank\",\n", " H9=\"IW-73.15\",\n", " H10=\"blank\",\n", " H11=\"IW-208.33\",\n", " H12=\"blank\",\n", ")" ] }, { "cell_type": "markdown", "id": "57f3892f-c43b-4941-abdb-9e7b1526105e", "metadata": {}, "source": [ "We should also store the promoter binding energy for each strain." ] }, { "cell_type": "code", "execution_count": 6, "id": "f361fbd3-f4ab-43ad-aa31-cb870d8c757c", "metadata": {}, "outputs": [], "source": [ "promoter_binding_energy = {\n", " 'blank': None,\n", " 'MG': np.inf,\n", " '3.19': -3.19,\n", " 'IW': -4.28,\n", " 'WT': -5.19,\n", " 'UV5': -7.93\n", "}" ] }, { "cell_type": "markdown", "id": "2b88f5cf-7c5a-43bc-bb16-8ed0d02f20d1", "metadata": {}, "source": [ "Now some functions to help us tidy the data set." ] }, { "cell_type": "code", "execution_count": 7, "id": "ee11d66d-1739-40db-bc0d-6db786c95572", "metadata": {}, "outputs": [], "source": [ "def conc(well, well_metadata):\n", " \"\"\"Return abx concentration for a given well\"\"\"\n", " strain_conc = well_metadata[well]\n", " if strain_conc == \"blank\":\n", " return 0.0\n", " else:\n", " ind = strain_conc.find(\"-\")\n", " return float(strain_conc[ind + 1 :])\n", "\n", "\n", "def strain(well, well_metadata):\n", " \"\"\"Return strain for a given well\"\"\"\n", " strain_conc = well_metadata[well]\n", " if strain_conc == \"blank\":\n", " return \"blank\"\n", " else:\n", " ind = strain_conc.find(\"-\")\n", " return strain_conc[:ind]\n", "\n", "\n", "def tidy(df, well_metadata, date):\n", " \"\"\"Convert data frame to tidy format.\"\"\"\n", " # Convert to tall format\n", " df_tidy = df.unpivot(\n", " index=[\"Time\", \"temperature (deg C)\", \"time (s)\", \"time (hr)\"],\n", " variable_name=\"well\",\n", " value_name=\"absorbance\",\n", " )\n", "\n", " # Add metadata columns\n", " df_tidy = df_tidy.with_columns(\n", " pl.col('well').map_elements(lambda x: conc(x, well_metadata), return_dtype=float).alias('conc'),\n", " pl.col('well').map_elements(lambda x: strain(x, well_metadata), return_dtype=str).alias('strain')\n", " ).with_columns(\n", " pl.col('strain').replace_strict(promoter_binding_energy, return_dtype=pl.Float64).alias('promoter_binding_energy')\n", " )\n", "\n", " # Add the date\n", " df_tidy = df_tidy.with_columns(date=pl.lit(date))\n", " \n", " # Sort, starting with promoter binding energy\n", " df_tidy = df_tidy.sort(\n", " by=[\"promoter_binding_energy\", \"conc\", \"well\", \"time (hr)\"]\n", " )\n", "\n", " return df_tidy" ] }, { "cell_type": "markdown", "id": "7697cfb0-432a-4f50-8043-451c2046d791", "metadata": {}, "source": [ "Now, tidy the date frame." ] }, { "cell_type": "code", "execution_count": 8, "id": "348715ab-915c-4a4e-ba85-9bd82b9cf002", "metadata": {}, "outputs": [], "source": [ "df = tidy(df, well_metadata, 20241122)" ] }, { "cell_type": "markdown", "id": "b75b569d-61ed-4ea6-b986-f53f870612c5", "metadata": {}, "source": [ "## We may also want to use last term's data\n", "\n", "To look at last term's data, you can directly load a tidy data frame as follows." ] }, { "cell_type": "code", "execution_count": 9, "id": "977c4b5f-4c7b-416b-beb4-47c54e4975a3", "metadata": {}, "outputs": [], "source": [ "df_spring = pl.read_csv(\n", " os.path.join(data_path, 'tidy_efflux_data_spring_2024.csv'),\n", " schema=df.schema\n", ")" ] }, { "cell_type": "markdown", "id": "979a2c72-0398-47d9-a691-156e28d2b407", "metadata": {}, "source": [ "We can put all the data in a single data frame if we want to analyze them all together." ] }, { "cell_type": "code", "execution_count": 10, "id": "6fa21c18-6ea5-41f5-a6e1-c7596667a07a", "metadata": {}, "outputs": [], "source": [ "df = pl.concat((df, df_spring))" ] }, { "cell_type": "markdown", "id": "e82e701e-5504-4ca2-80c3-59bad9e3a772", "metadata": {}, "source": [ "We could us all of the data, or pull out a specific experiment. To pull out a specific experiment, we can do it by date. We will use this term's data." ] }, { "cell_type": "code", "execution_count": 11, "id": "2f4f5665-575f-4b46-abc1-24d0c19c01f1", "metadata": {}, "outputs": [], "source": [ "# To pull out the spring data use\n", "# df = df.filter(pl.col('date')<20241122)\n", "\n", "df = df.filter(pl.col('date')==20241122)" ] }, { "cell_type": "markdown", "id": "31e6b6b9-e79e-4196-82f4-6aa74c528504", "metadata": {}, "source": [ "## Checking the blanks\n", "\n", "Let's check all blanks. Group A is colored blue and group B red." ] }, { "cell_type": "code", "execution_count": 12, "id": "d9955e6b-d358-4b9a-b3b4-273e7703f9c1", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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calculations.\n", "\n", "We can now subtract the blanks to get the OD600." ] }, { "cell_type": "code", "execution_count": 13, "id": "1c82f536-2e72-48fc-8d44-cf7ac69387cd", "metadata": {}, "outputs": [], "source": [ "# ##################\n", "# You need to give an explanation of what the code in this cell is doing.\n", "# ##################\n", "\n", "# Compute blanks\n", "blank = df.filter((pl.col(\"strain\") == \"blank\") & (pl.col('well') != 'H12'))[\"absorbance\"].mean()\n", "\n", "# Subtract blanks\n", "df = df.with_columns((pl.col('absorbance') - blank).alias('OD600'))\n", "\n", "# Clean out negative values\n", "df = df.filter(pl.col('OD600') > 0)" ] }, { "cell_type": "markdown", "id": "ecc875db-2f44-4593-9fbb-5429b755e4e7", "metadata": {}, "source": [ "## Plotting the curves\n", "\n", "We now write a function to plot all curves (except blanks) for each concentration of antibiotic." ] }, { "cell_type": "code", "execution_count": 14, "id": "5a8ba5e1-dde5-48b5-9480-33cd6d465250", "metadata": {}, "outputs": [], "source": [ "def plot_curves(df, conc):\n", " p = bokeh.plotting.figure(\n", " frame_width=400,\n", " frame_height=250,\n", " x_axis_label=\"time (hr)\",\n", " y_axis_label=\"OD600\",\n", " y_axis_type=\"log\",\n", " toolbar_location=\"above\",\n", " tooltips=[('well', '@well')],\n", " title=f'conc = {conc} µM',\n", " )\n", " \n", " # Color scheme\n", " colors = bokeh.palettes.Category10_10\n", " \n", " # Pull out only entries for antibiotic concentration of interest (and not blanks)\n", " inds = (pl.col(\"conc\") == conc) & (pl.col(\"strain\") != \"blank\")\n", " df_conc = df.filter(inds)\n", " \n", " # Items we will place in the legend\n", " legend_items = []\n", " \n", " # Groupby and iterate, adding to plot\n", " color_index = 0\n", " for (strain,), sub_df in df_conc.group_by(\"strain\", maintain_order=True):\n", " # Lines for a given strain\n", " lines = []\n", " \n", " # Get each well for the strain and add a line to the plot\n", " for well, subsub_df in sub_df.group_by(\"well\", maintain_order=True):\n", " lines.append(\n", " p.line(source=subsub_df.to_dict(), x=\"time (hr)\", y=\"OD600\", color=colors[color_index])\n", " )\n", " \n", " color_index += 1\n", " \n", " # Add the lines to the legend\n", " legend_items.append((strain, lines))\n", " \n", " # Create the legend from the items\n", " legend = bokeh.models.Legend(items=legend_items, click_policy=\"hide\")\n", " \n", " # Add the legend to the plot\n", " p.add_layout(legend, \"right\")\n", "\n", " return p" ] }, { "cell_type": "markdown", "id": "beffbbf5-f019-4b03-9131-7e5c9c855edf", "metadata": {}, "source": [ "We can then use this to make a plot of all curves. For convenience, we make a plot with tabs containing each concentration. This is also a useful visualization simply to see the growth curves." ] }, { "cell_type": "code", "execution_count": 15, "id": "6853680c-93fe-4caa-96f5-3a8ff7310413", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
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(hr)\",\"major_label_policy\":{\"type\":\"object\",\"name\":\"AllLabels\",\"id\":\"p2675\"}}}],\"center\":[{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p2676\",\"attributes\":{\"axis\":{\"id\":\"p2672\"}}},{\"type\":\"object\",\"name\":\"Grid\",\"id\":\"p2681\",\"attributes\":{\"dimension\":1,\"axis\":{\"id\":\"p2677\"}}}],\"frame_width\":400,\"frame_height\":250}}}}]}}]}};\n", " const render_items = [{\"docid\":\"60816c0e-9982-4d11-a3fc-ad1680368422\",\"roots\":{\"p2762\":\"e2241381-33bc-4af7-a7cc-8a23b02c0191\"},\"root_ids\":[\"p2762\"]}];\n", " void root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " let attempts = 0;\n", " const timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " clearInterval(timer);\n", " embed_document(root);\n", " } else {\n", " attempts++;\n", " if (attempts > 100) {\n", " clearInterval(timer);\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " }\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "p2762" } }, "output_type": "display_data" } ], "source": [ "tabs = []\n", "for c in df['conc'].unique():\n", " tabs.append(bokeh.models.TabPanel(child=plot_curves(df, c), title=str(c)))\n", "\n", "all_plots = bokeh.models.Tabs(tabs=tabs)\n", "bokeh.io.show(bokeh.models.Tabs(tabs=tabs))" ] }, { "cell_type": "markdown", "id": "4bbb4b5f-190e-4c43-9e1d-bb66c136b5f7", "metadata": {}, "source": [ "In all curves, if there is growth, it is exponential between OD of 0.15 and 0.3." ] }, { "cell_type": "markdown", "id": "89075686-a7b0-48f9-a55e-f9e48f0c7704", "metadata": {}, "source": [ "## Obtaining growth rate\n", "\n", "Below are functions to help with the regressions to obtain growth rates." ] }, { "cell_type": "code", "execution_count": 16, "id": "43d3986b-4d21-4413-a6a3-c1fb4e8bb290", "metadata": {}, "outputs": [], "source": [ "def exp_growth(t, A0, lam):\n", " return A0 * np.exp(lam * t)\n", "\n", "\n", "def fit_growth(t, OD, ODmin=0.15, ODmax=0.3):\n", " \"\"\"Obtain estimates for A0 and λ for a given sub-trace\"\"\"\n", " # Pull out linear regime\n", " inds = np.logical_and(OD >= ODmin, OD <= ODmax)\n", " t = t[inds]\n", " OD = OD[inds]\n", " \n", " # If no growth, return zero\n", " if len(t) == 0:\n", " return 0.0\n", " \n", " # Parameter guesses\n", " A0_guess = 0.01\n", " lam_guess = 1.0 # 1/hr\n", "\n", " # Perform optimization\n", " popt, _ = scipy.optimize.curve_fit(exp_growth, t, OD, p0=(A0_guess, lam_guess))\n", " \n", " # Just return growth rate \n", " return popt[1]" ] }, { "cell_type": "markdown", "id": "eaa550b6-879b-4d6e-a4cf-7f1c5546ecda", "metadata": {}, "source": [ "As an example, I show how to compute growth rates for all strains with zero antibiotic concentration." ] }, { "cell_type": "code", "execution_count": 17, "id": "61aa9b1c-e6a7-4c5c-a7d0-3597e0f616ff", "metadata": {}, "outputs": [], "source": [ "# ##################\n", "# You need to give an explanation of what the code in this cell is doing.\n", "# ##################\n", "\n", "# Pull out only entries for zero antibiotic concentration (and not blanks)\n", "df_0abx = df.filter((pl.col(\"conc\") == 0.0) & (pl.col(\"strain\") != \"blank\"))\n", "\n", "# Compute growth rates\n", "growth_rates_0abx = (\n", " df_0abx.group_by([\"strain\", \"well\"], maintain_order=True)\n", " .agg(\n", " pl.struct([\"time (hr)\", \"OD600\"]).map_elements(\n", " lambda s: fit_growth(\n", " s.struct.field(\"time (hr)\").to_numpy(),\n", " s.struct.field(\"OD600\").to_numpy(),\n", " ),\n", " return_dtype=float,\n", " returns_scalar=True,\n", " )\n", " .alias(\"growth rate (1/hr)\")\n", " )\n", ")" ] }, { "cell_type": "code", "execution_count": 18, "id": "f6c39d69-38e8-437f-a380-80bda82a74dc", "metadata": {}, "outputs": [ { "data": { 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………
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"UV5"0.370197
"WT"0.408679
" ], "text/plain": [ "shape: (5, 2)\n", "┌────────┬──────────┐\n", "│ strain ┆ lam0 │\n", "│ --- ┆ --- │\n", "│ str ┆ f64 │\n", "╞════════╪══════════╡\n", "│ IW ┆ 0.494827 │\n", "│ 3.19 ┆ 0.504496 │\n", "│ MG ┆ 0.552755 │\n", "│ UV5 ┆ 0.370197 │\n", "│ WT ┆ 0.408679 │\n", "└────────┴──────────┘" ] }, "execution_count": 20, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# ##################\n", "# You need to give an explanation of what the code in this cell is doing.\n", "# ##################\n", "\n", "lam0 = growth_rates_0abx.group_by(\"strain\").agg(\n", " pl.col(\"growth rate (1/hr)\").median().alias(\"lam0\")\n", ")\n", "\n", "# Take a look\n", "lam0" ] }, { "cell_type": "markdown", "id": "6bbb93aa-b949-409b-8f80-ecf85e39c862", "metadata": {}, "source": [ "Perhaps unsurprisingly, the growth rates are all similar. For convenience, let's add these to the data frame." ] }, { "cell_type": "code", "execution_count": 21, "id": "da732d5c-0513-411e-b72d-6f11a6f226f8", "metadata": {}, "outputs": [], "source": [ "df = df.join(lam0, on='strain')" ] }, { "cell_type": "markdown", "id": "2705b47a-e254-46eb-ac22-8836d4fb3d5c", "metadata": {}, "source": [ "## Solver for theoretical growth rate\n", "\n", "Recall from the theory that the growth rate $\\lambda$ is found by solving a cubic equation. The following functions may be used to perform that solution. Be sure to read these carefully to understand how they work." ] }, { "cell_type": "code", "execution_count": 22, "id": "6dfa067f-7b2c-4949-826b-f5437251039e", "metadata": {}, "outputs": [], "source": [ "def solve_growth_rate_dimensionless(\n", " aex, kappa, K, qmax, Pin, Pout, return_all_roots=False\n", "):\n", " \"\"\"Solve for the growth rate for a single antibiotic\n", " concentation in dimensionless units. All parameters\n", " are dimensionless. If `return_all_roots` is True,\n", " returns all physically viable steady state growth rates.\n", " Otherwise, only the single stable growth rate is returned.\n", " \"\"\"\n", " # No antibiotic: max growth rate\n", " if aex == 0.0:\n", " lam = np.array([1.0])\n", " else:\n", " # Coefficients for cubic polynomial\n", " a3 = K + qmax - 1\n", " a2 = 2 - (1 - K) * (Pin * aex + Pout) - (1 - kappa) * (qmax + K)\n", " a1 = (\n", " -1\n", " - kappa * (qmax + K)\n", " + (2 - (1 - kappa) * K) * Pout\n", " + (1 - (1 - 2 * K) * kappa) * Pin * aex\n", " )\n", " a0 = (1 + kappa * K) * (kappa * Pin * aex - Pout)\n", "\n", " # Set up the cubic polynomial\n", " cubic = np.polynomial.Polynomial([a0, a1, a2, a3])\n", "\n", " # Solve the cubic\n", " lam = np.sort([r for r in cubic.roots() if np.isreal(r) and 0 <= r <= 1])\n", "\n", " # No roots, return 0\n", " if len(lam) == 0:\n", " return 0.0\n", "\n", " if return_all_roots:\n", " return lam if len(lam) > 1 else lam[0]\n", " else:\n", " return lam[-1]\n", "\n", "\n", "def growth_rate(\n", " aex, # µM\n", " qmax, # µM/hr\n", " lam0, # 1/hr\n", " rmin=19.3, # µM\n", " kappa_t=0.061, # 1/µM\n", " Pin=2.85, # 1/hr\n", " Pout=2.85, # 1/hr\n", " Kd=1.0, # µM\n", " KM=10.0, # µM\n", "):\n", " \"\"\"Solve for the growth rate for antibiotic concentration, or\n", " array of antibiotic concentrations, aex. Assumes all\n", " concentration units are µM and all time units are hours.\n", " \"\"\"\n", " # Nondimensionalize\n", " kappa = kappa_t * rmin / lam0\n", " K = KM / Kd\n", " qmax = qmax / Kd / lam0\n", " Pin = Pin / lam0\n", " Pout = Pout / lam0\n", " aex = aex / Kd\n", "\n", " if np.isscalar(aex):\n", " result = solve_growth_rate_dimensionless(\n", " aex, kappa, K, qmax, Pin, Pout, return_all_roots=False\n", " )\n", " else:\n", " result = [\n", " solve_growth_rate_dimensionless(\n", " aex_val, kappa, K, qmax, Pin, Pout, return_all_roots=False\n", " )\n", " for aex_val in aex\n", " ]\n", " result = np.array(result)\n", "\n", " # Return dimensional growth rate\n", " return result * lam0" ] }, { "cell_type": "markdown", "id": "2fb6bae7-087f-492e-9fd3-c8ef02124630", "metadata": {}, "source": [ "You can now proceed with the analysis!" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.12.5" } }, "nbformat": 4, "nbformat_minor": 5 }